Opened 3 years ago

Closed 2 years ago

Last modified 2 years ago

#6910 closed defect (fixed)

XMAS: KeyError: 'Score'

Reported by: chimerax-bug-report@… Owned by: Richard Scheltema
Priority: normal Milestone:
Component: Third Party Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Windows-10-10.0.17763
ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> help help:user

> open C:/Users/TColby/Documents/C2H2Motif/RNF114_25-112.pdb

RNF114_25-112.pdb title:  
Alphafold monomer V2.0 prediction for E3 ubiquitin-protein ligase RNF114
(Q9Y508) [more info...]  
  
Chain information for RNF114_25-112.pdb #1  
---  
Chain | Description | UniProt  
A | E3 ubiquitin-protein ligase RNF114 | RN114_HUMAN  
  

> open C:/Users/TColby/Documents/C2H2Motif/RNF114_25-112.pdb

RNF114_25-112.pdb title:  
Alphafold monomer V2.0 prediction for E3 ubiquitin-protein ligase RNF114
(Q9Y508) [more info...]  
  
Chain information for RNF114_25-112.pdb #2  
---  
Chain | Description | UniProt  
A | E3 ubiquitin-protein ligase RNF114 | RN114_HUMAN  
  

> close #2

> open C:/Users/TColby/Documents/C2H2Motif/RNF114_140-200.pdb

RNF114_140-200.pdb title:  
Alphafold monomer V2.0 prediction for E3 ubiquitin-protein ligase RNF114
(Q9Y508) [more info...]  
  
Chain information for RNF114_140-200.pdb #2  
---  
Chain | Description | UniProt  
A | E3 ubiquitin-protein ligase RNF114 | RN114_HUMAN  
  

> toolshed show

> ui tool show ViewDockX

No suitable models found for ViewDockX  
Downloading bundle ChimeraX_XMAS-1.1.1-py3-none-any.whl  
[Repeated 1 time(s)]

Errors may have occurred when running pip:  

pip standard error:  
\---  
WARNING: Value for scheme.platlib does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>  
distutils: C:\Users\TColby\AppData\Local\UCSF\ChimeraX\1.3\site-packages  
sysconfig: C:\Users\TColby\AppData\Roaming\Python\Python39\site-packages  
WARNING: Value for scheme.purelib does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>  
distutils: C:\Users\TColby\AppData\Local\UCSF\ChimeraX\1.3\site-packages  
sysconfig: C:\Users\TColby\AppData\Roaming\Python\Python39\site-packages  
WARNING: Value for scheme.headers does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>  
distutils: C:\Users\TColby\AppData\Local\UCSF\ChimeraX\Python39\Include\pandas  
sysconfig: C:\Users\TColby\AppData\Roaming\Python\Python39\Include\pandas  
WARNING: Value for scheme.scripts does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>  
distutils: C:\Users\TColby\AppData\Local\UCSF\ChimeraX\Python39\Scripts  
sysconfig: C:\Users\TColby\AppData\Roaming\Python\Python39\Scripts  
WARNING: Value for scheme.data does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>  
distutils: C:\Users\TColby\AppData\Local\UCSF\ChimeraX  
sysconfig: C:\Users\TColby\AppData\Roaming\Python  
WARNING: Additional context:  
user = True  
home = None  
root = None  
prefix = None  
WARNING: Value for scheme.headers does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>  
distutils: C:\Users\TColby\AppData\Local\UCSF\ChimeraX\Python39\Include\et-
xmlfile  
sysconfig: C:\Users\TColby\AppData\Roaming\Python\Python39\Include\et-xmlfile  
WARNING: Value for scheme.headers does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>  
distutils:
C:\Users\TColby\AppData\Local\UCSF\ChimeraX\Python39\Include\seaborn  
sysconfig: C:\Users\TColby\AppData\Roaming\Python\Python39\Include\seaborn  
WARNING: Value for scheme.headers does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>  
distutils:
C:\Users\TColby\AppData\Local\UCSF\ChimeraX\Python39\Include\qtrangeslider  
sysconfig:
C:\Users\TColby\AppData\Roaming\Python\Python39\Include\qtrangeslider  
WARNING: Value for scheme.headers does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>  
distutils:
C:\Users\TColby\AppData\Local\UCSF\ChimeraX\Python39\Include\openpyxl  
sysconfig: C:\Users\TColby\AppData\Roaming\Python\Python39\Include\openpyxl  
WARNING: Value for scheme.headers does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>  
distutils:
C:\Users\TColby\AppData\Local\UCSF\ChimeraX\Python39\Include\ChimeraX-XMAS  
sysconfig: C:\Users\TColby\AppData\Roaming\Python\Python39\Include\ChimeraX-
XMAS  
WARNING: Value for scheme.headers does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>  
distutils:
C:\Users\TColby\AppData\Local\UCSF\ChimeraX\Python39\Include\UNKNOWN  
sysconfig: C:\Users\TColby\AppData\Roaming\Python\Python39\Include\UNKNOWN  
WARNING: You are using pip version 21.2.4; however, version 22.1 is available.  
You should consider upgrading via the 'C:\Program Files\ChimeraX
1.3\bin\ChimeraX.exe -m pip install --upgrade pip' command.  
\---  

pip standard output:  
\---  
Looking in indexes: https://pypi.org/simple,
https://cxtoolshed.rbvi.ucsf.edu/pypi/  
Processing c:\users\tcolby\downloads\chimerax_xmas-1.1.1-py3-none-any.whl  
Collecting seaborn  
Downloading seaborn-0.11.2-py3-none-any.whl (292 kB)  
Requirement already satisfied: ChimeraX-UI~=1.3 in c:\program files\chimerax
1.3\bin\lib\site-packages (from ChimeraX-XMAS==1.1.1) (1.13.7)  
Collecting qtrangeslider  
Downloading QtRangeSlider-0.1.5-py3-none-any.whl (33 kB)  
Requirement already satisfied: ChimeraX-Core~=1.3 in c:\program files\chimerax
1.3\bin\lib\site-packages (from ChimeraX-XMAS==1.1.1) (1.3)  
Collecting pandas  
Downloading pandas-1.4.2-cp39-cp39-win_amd64.whl (10.5 MB)  
Collecting openpyxl  
Downloading openpyxl-3.0.9-py2.py3-none-any.whl (242 kB)  
Requirement already satisfied: ChimeraX-SelInspector~=1.0 in c:\program
files\chimerax 1.3\bin\lib\site-packages (from ChimeraX-UI~=1.3->ChimeraX-
XMAS==1.1.1) (1.0)  
Requirement already satisfied: ChimeraX-Graphics~=1.0 in c:\program
files\chimerax 1.3\bin\lib\site-packages (from ChimeraX-UI~=1.3->ChimeraX-
XMAS==1.1.1) (1.1)  
Requirement already satisfied: ChimeraX-MouseModes~=1.0 in c:\program
files\chimerax 1.3\bin\lib\site-packages (from ChimeraX-UI~=1.3->ChimeraX-
XMAS==1.1.1) (1.1)  
Requirement already satisfied: ChimeraX-Geometry~=1.0 in c:\program
files\chimerax 1.3\bin\lib\site-packages (from ChimeraX-
Graphics~=1.0->ChimeraX-UI~=1.3->ChimeraX-XMAS==1.1.1) (1.1)  
Requirement already satisfied: ChimeraX-Arrays~=1.0 in c:\program
files\chimerax 1.3\bin\lib\site-packages (from ChimeraX-
Graphics~=1.0->ChimeraX-UI~=1.3->ChimeraX-XMAS==1.1.1) (1.0)  
Requirement already satisfied: ChimeraX-ItemsInspection~=1.0 in c:\program
files\chimerax 1.3\bin\lib\site-packages (from ChimeraX-
SelInspector~=1.0->ChimeraX-UI~=1.3->ChimeraX-XMAS==1.1.1) (1.0)  
Collecting et-xmlfile  
Downloading et_xmlfile-1.1.0-py3-none-any.whl (4.7 kB)  
Requirement already satisfied: pytz>=2020.1 in c:\program files\chimerax
1.3\bin\lib\site-packages (from pandas->ChimeraX-XMAS==1.1.1) (2021.3)  
Requirement already satisfied: python-dateutil>=2.8.1 in c:\program
files\chimerax 1.3\bin\lib\site-packages (from pandas->ChimeraX-XMAS==1.1.1)
(2.8.2)  
Requirement already satisfied: numpy>=1.18.5 in c:\program files\chimerax
1.3\bin\lib\site-packages (from pandas->ChimeraX-XMAS==1.1.1) (1.21.2)  
Requirement already satisfied: six>=1.5 in c:\program files\chimerax
1.3\bin\lib\site-packages (from python-dateutil>=2.8.1->pandas->ChimeraX-
XMAS==1.1.1) (1.16.0)  
Requirement already satisfied: matplotlib>=2.2 in c:\program files\chimerax
1.3\bin\lib\site-packages (from seaborn->ChimeraX-XMAS==1.1.1) (3.4.3)  
Requirement already satisfied: scipy>=1.0 in c:\program files\chimerax
1.3\bin\lib\site-packages (from seaborn->ChimeraX-XMAS==1.1.1) (1.7.1)  
Requirement already satisfied: kiwisolver>=1.0.1 in c:\program files\chimerax
1.3\bin\lib\site-packages (from matplotlib>=2.2->seaborn->ChimeraX-
XMAS==1.1.1) (1.3.2)  
Requirement already satisfied: cycler>=0.10 in c:\program files\chimerax
1.3\bin\lib\site-packages (from matplotlib>=2.2->seaborn->ChimeraX-
XMAS==1.1.1) (0.11.0)  
Requirement already satisfied: pyparsing>=2.2.1 in c:\program files\chimerax
1.3\bin\lib\site-packages (from matplotlib>=2.2->seaborn->ChimeraX-
XMAS==1.1.1) (3.0.6)  
Requirement already satisfied: pillow>=6.2.0 in c:\program files\chimerax
1.3\bin\lib\site-packages (from matplotlib>=2.2->seaborn->ChimeraX-
XMAS==1.1.1) (8.3.2)  
Installing collected packages: pandas, et-xmlfile, seaborn, qtrangeslider,
openpyxl, ChimeraX-XMAS  
Successfully installed ChimeraX-XMAS-1.1.1 et-xmlfile-1.1.0 openpyxl-3.0.9
pandas-1.4.2 qtrangeslider-0.1.5 seaborn-0.11.2  
\---  

Successfully installed ChimeraX-XMAS-1.1.1 et-xmlfile-1.1.0 openpyxl-3.0.9
pandas-1.4.2 qtrangeslider-0.1.5 seaborn-0.11.2  
Installed ChimeraX-XMAS (1.1.1)  

> ui tool show XMAS

Please check one or more files  

> help help:user

Traceback (most recent call last):  
File "C:\Users\TColby\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\pandas\core\indexes\base.py", line 3621, in get_loc  
return self._engine.get_loc(casted_key)  
File "pandas\\_libs\index.pyx", line 136, in
pandas._libs.index.IndexEngine.get_loc  
File "pandas\\_libs\index.pyx", line 163, in
pandas._libs.index.IndexEngine.get_loc  
File "pandas\\_libs\hashtable_class_helper.pxi", line 5198, in
pandas._libs.hashtable.PyObjectHashTable.get_item  
File "pandas\\_libs\hashtable_class_helper.pxi", line 5206, in
pandas._libs.hashtable.PyObjectHashTable.get_item  
KeyError: 'Score'  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File "C:\Users\TColby\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\xmas\tool.py", line 285, in <lambda>  
function = lambda _, s=selector, t=key: self.map_button_clicked(s,  
File "C:\Users\TColby\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\xmas\tool.py", line 443, in map_button_clicked  
self.map_crosslinks(self.checked_models, checked_files)  
File "C:\Users\TColby\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\xmas\tool.py", line 456, in map_crosslinks  
evidence = Evidence(evidence_file)  
File "C:\Users\TColby\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\xmas\read_evidence.py", line 37, in __init__  
evidence = cls(evidence_file)  
File "C:\Users\TColby\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\xmas\read_evidence.py", line 102, in __init__  
df = self.make_df(evidence_file, delimiter, header)  
File "C:\Users\TColby\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\xmas\read_evidence.py", line 282, in make_df  
if (df[score_col].dtypes != "float64" and delimiter != ","):  
File "C:\Users\TColby\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\pandas\core\frame.py", line 3505, in __getitem__  
indexer = self.columns.get_loc(key)  
File "C:\Users\TColby\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\pandas\core\indexes\base.py", line 3623, in get_loc  
raise KeyError(key) from err  
KeyError: 'Score'  
  
KeyError: 'Score'  
  
File "C:\Users\TColby\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\pandas\core\indexes\base.py", line 3623, in get_loc  
raise KeyError(key) from err  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Users\TColby\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\pandas\core\indexes\base.py", line 3621, in get_loc  
return self._engine.get_loc(casted_key)  
File "pandas\\_libs\index.pyx", line 136, in
pandas._libs.index.IndexEngine.get_loc  
File "pandas\\_libs\index.pyx", line 163, in
pandas._libs.index.IndexEngine.get_loc  
File "pandas\\_libs\hashtable_class_helper.pxi", line 5198, in
pandas._libs.hashtable.PyObjectHashTable.get_item  
File "pandas\\_libs\hashtable_class_helper.pxi", line 5206, in
pandas._libs.hashtable.PyObjectHashTable.get_item  
KeyError: 'Score'  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File "C:\Users\TColby\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\xmas\tool.py", line 285, in <lambda>  
function = lambda _, s=selector, t=key: self.map_button_clicked(s,  
File "C:\Users\TColby\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\xmas\tool.py", line 443, in map_button_clicked  
self.map_crosslinks(self.checked_models, checked_files)  
File "C:\Users\TColby\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\xmas\tool.py", line 456, in map_crosslinks  
evidence = Evidence(evidence_file)  
File "C:\Users\TColby\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\xmas\read_evidence.py", line 37, in __init__  
evidence = cls(evidence_file)  
File "C:\Users\TColby\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\xmas\read_evidence.py", line 102, in __init__  
df = self.make_df(evidence_file, delimiter, header)  
File "C:\Users\TColby\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\xmas\read_evidence.py", line 282, in make_df  
if (df[score_col].dtypes != "float64" and delimiter != ","):  
File "C:\Users\TColby\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\pandas\core\frame.py", line 3505, in __getitem__  
indexer = self.columns.get_loc(key)  
File "C:\Users\TColby\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\pandas\core\indexes\base.py", line 3623, in get_loc  
raise KeyError(key) from err  
KeyError: 'Score'  
  
KeyError: 'Score'  
  
File "C:\Users\TColby\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\pandas\core\indexes\base.py", line 3623, in get_loc  
raise KeyError(key) from err  
  
See log for complete Python traceback.  
  

> open
> C:/Users/TColby/Documents/C2H2Motif/FromCarolinasFriend/AF-Q9Y508-F1-model_v2.pdb

AF-Q9Y508-F1-model_v2.pdb title:  
Alphafold monomer V2.0 prediction for E3 ubiquitin-protein ligase RNF114
(Q9Y508) [more info...]  
  
Chain information for AF-Q9Y508-F1-model_v2.pdb #3  
---  
Chain | Description | UniProt  
A | E3 ubiquitin-protein ligase RNF114 | RN114_HUMAN  
  
Traceback (most recent call last):  
File "C:\Users\TColby\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\pandas\core\indexes\base.py", line 3621, in get_loc  
return self._engine.get_loc(casted_key)  
File "pandas\\_libs\index.pyx", line 136, in
pandas._libs.index.IndexEngine.get_loc  
File "pandas\\_libs\index.pyx", line 163, in
pandas._libs.index.IndexEngine.get_loc  
File "pandas\\_libs\hashtable_class_helper.pxi", line 5198, in
pandas._libs.hashtable.PyObjectHashTable.get_item  
File "pandas\\_libs\hashtable_class_helper.pxi", line 5206, in
pandas._libs.hashtable.PyObjectHashTable.get_item  
KeyError: 'Score'  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File "C:\Users\TColby\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\xmas\tool.py", line 285, in <lambda>  
function = lambda _, s=selector, t=key: self.map_button_clicked(s,  
File "C:\Users\TColby\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\xmas\tool.py", line 443, in map_button_clicked  
self.map_crosslinks(self.checked_models, checked_files)  
File "C:\Users\TColby\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\xmas\tool.py", line 456, in map_crosslinks  
evidence = Evidence(evidence_file)  
File "C:\Users\TColby\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\xmas\read_evidence.py", line 37, in __init__  
evidence = cls(evidence_file)  
File "C:\Users\TColby\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\xmas\read_evidence.py", line 102, in __init__  
df = self.make_df(evidence_file, delimiter, header)  
File "C:\Users\TColby\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\xmas\read_evidence.py", line 282, in make_df  
if (df[score_col].dtypes != "float64" and delimiter != ","):  
File "C:\Users\TColby\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\pandas\core\frame.py", line 3505, in __getitem__  
indexer = self.columns.get_loc(key)  
File "C:\Users\TColby\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\pandas\core\indexes\base.py", line 3623, in get_loc  
raise KeyError(key) from err  
KeyError: 'Score'  
  
KeyError: 'Score'  
  
File "C:\Users\TColby\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\pandas\core\indexes\base.py", line 3623, in get_loc  
raise KeyError(key) from err  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Users\TColby\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\pandas\core\indexes\base.py", line 3621, in get_loc  
return self._engine.get_loc(casted_key)  
File "pandas\\_libs\index.pyx", line 136, in
pandas._libs.index.IndexEngine.get_loc  
File "pandas\\_libs\index.pyx", line 163, in
pandas._libs.index.IndexEngine.get_loc  
File "pandas\\_libs\hashtable_class_helper.pxi", line 5198, in
pandas._libs.hashtable.PyObjectHashTable.get_item  
File "pandas\\_libs\hashtable_class_helper.pxi", line 5206, in
pandas._libs.hashtable.PyObjectHashTable.get_item  
KeyError: 'Score'  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File "C:\Users\TColby\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\xmas\tool.py", line 285, in <lambda>  
function = lambda _, s=selector, t=key: self.map_button_clicked(s,  
File "C:\Users\TColby\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\xmas\tool.py", line 443, in map_button_clicked  
self.map_crosslinks(self.checked_models, checked_files)  
File "C:\Users\TColby\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\xmas\tool.py", line 456, in map_crosslinks  
evidence = Evidence(evidence_file)  
File "C:\Users\TColby\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\xmas\read_evidence.py", line 37, in __init__  
evidence = cls(evidence_file)  
File "C:\Users\TColby\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\xmas\read_evidence.py", line 102, in __init__  
df = self.make_df(evidence_file, delimiter, header)  
File "C:\Users\TColby\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\xmas\read_evidence.py", line 282, in make_df  
if (df[score_col].dtypes != "float64" and delimiter != ","):  
File "C:\Users\TColby\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\pandas\core\frame.py", line 3505, in __getitem__  
indexer = self.columns.get_loc(key)  
File "C:\Users\TColby\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\pandas\core\indexes\base.py", line 3623, in get_loc  
raise KeyError(key) from err  
KeyError: 'Score'  
  
KeyError: 'Score'  
  
File "C:\Users\TColby\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\pandas\core\indexes\base.py", line 3623, in get_loc  
raise KeyError(key) from err  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Users\TColby\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\pandas\core\indexes\base.py", line 3621, in get_loc  
return self._engine.get_loc(casted_key)  
File "pandas\\_libs\index.pyx", line 136, in
pandas._libs.index.IndexEngine.get_loc  
File "pandas\\_libs\index.pyx", line 163, in
pandas._libs.index.IndexEngine.get_loc  
File "pandas\\_libs\hashtable_class_helper.pxi", line 5198, in
pandas._libs.hashtable.PyObjectHashTable.get_item  
File "pandas\\_libs\hashtable_class_helper.pxi", line 5206, in
pandas._libs.hashtable.PyObjectHashTable.get_item  
KeyError: 'PSMID'  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File "C:\Users\TColby\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\xmas\tool.py", line 285, in <lambda>  
function = lambda _, s=selector, t=key: self.map_button_clicked(s,  
File "C:\Users\TColby\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\xmas\tool.py", line 443, in map_button_clicked  
self.map_crosslinks(self.checked_models, checked_files)  
File "C:\Users\TColby\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\xmas\tool.py", line 456, in map_crosslinks  
evidence = Evidence(evidence_file)  
File "C:\Users\TColby\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\xmas\read_evidence.py", line 37, in __init__  
evidence = cls(evidence_file)  
File "C:\Users\TColby\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\xmas\read_evidence.py", line 106, in __init__  
self.engines[engine][1](df)  
File "C:\Users\TColby\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\xmas\read_evidence.py", line 132, in parse_pd_xi_seqs_scores  
function(peptide_pairs, df, xi_alternative)  
File "C:\Users\TColby\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\xmas\read_evidence.py", line 219, in parse_xi_pos_ids  
params[key] = df[col_name].tolist()  
File "C:\Users\TColby\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\pandas\core\frame.py", line 3505, in __getitem__  
indexer = self.columns.get_loc(key)  
File "C:\Users\TColby\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\pandas\core\indexes\base.py", line 3623, in get_loc  
raise KeyError(key) from err  
KeyError: 'PSMID'  
  
KeyError: 'PSMID'  
  
File "C:\Users\TColby\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\pandas\core\indexes\base.py", line 3623, in get_loc  
raise KeyError(key) from err  
  
See log for complete Python traceback.  
  
Please select pseudobonds  
Traceback (most recent call last):  
File "C:\Users\TColby\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\pandas\core\indexes\base.py", line 3621, in get_loc  
return self._engine.get_loc(casted_key)  
File "pandas\\_libs\index.pyx", line 136, in
pandas._libs.index.IndexEngine.get_loc  
File "pandas\\_libs\index.pyx", line 163, in
pandas._libs.index.IndexEngine.get_loc  
File "pandas\\_libs\hashtable_class_helper.pxi", line 5198, in
pandas._libs.hashtable.PyObjectHashTable.get_item  
File "pandas\\_libs\hashtable_class_helper.pxi", line 5206, in
pandas._libs.hashtable.PyObjectHashTable.get_item  
KeyError: 'Score'  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File "C:\Users\TColby\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\xmas\tool.py", line 285, in <lambda>  
function = lambda _, s=selector, t=key: self.map_button_clicked(s,  
File "C:\Users\TColby\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\xmas\tool.py", line 443, in map_button_clicked  
self.map_crosslinks(self.checked_models, checked_files)  
File "C:\Users\TColby\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\xmas\tool.py", line 456, in map_crosslinks  
evidence = Evidence(evidence_file)  
File "C:\Users\TColby\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\xmas\read_evidence.py", line 37, in __init__  
evidence = cls(evidence_file)  
File "C:\Users\TColby\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\xmas\read_evidence.py", line 102, in __init__  
df = self.make_df(evidence_file, delimiter, header)  
File "C:\Users\TColby\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\xmas\read_evidence.py", line 282, in make_df  
if (df[score_col].dtypes != "float64" and delimiter != ","):  
File "C:\Users\TColby\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\pandas\core\frame.py", line 3505, in __getitem__  
indexer = self.columns.get_loc(key)  
File "C:\Users\TColby\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\pandas\core\indexes\base.py", line 3623, in get_loc  
raise KeyError(key) from err  
KeyError: 'Score'  
  
KeyError: 'Score'  
  
File "C:\Users\TColby\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\pandas\core\indexes\base.py", line 3623, in get_loc  
raise KeyError(key) from err  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 - Build 30.0.100.9864
OpenGL renderer: Intel(R) UHD Graphics 630
OpenGL vendor: Intel
Manufacturer: Dell Inc.
Model: OptiPlex 3070
OS: Microsoft Windows 10 Enterprise LTSC (Build 17763)
Memory: 16,979,660,800
MaxProcessMemory: 137,438,953,344
CPU: 6 Intel(R) Core(TM) i5-9600T CPU @ 2.30GHz
OSLanguage: en-US
Locale: ('en_US', 'cp1252')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2021.10.8
    cftime: 1.5.1.1
    charset-normalizer: 2.0.9
    ChimeraX-AddCharge: 1.2.2
    ChimeraX-AddH: 2.1.11
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.2.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.31
    ChimeraX-AtomicLibrary: 4.2
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.0
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.6.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.2
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.2
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5
    ChimeraX-CommandLine: 1.1.5
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.3
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.5
    ChimeraX-DistUI: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.1
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
    ChimeraX-Hbonds: 2.1.2
    ChimeraX-Help: 1.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0
    ChimeraX-Label: 1.1
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.4
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 2.0.4
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.4
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.2.6
    ChimeraX-ModelPanel: 1.2.1
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.2
    ChimeraX-OpenCommand: 1.7
    ChimeraX-PDB: 2.6.5
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0.1
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.4.6
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.1
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.6.1
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.13.7
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.0.1
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.0
    ChimeraX-XMAS: 1.1.1
    ChimeraX-Zone: 1.0
    colorama: 0.4.4
    comtypes: 1.1.10
    cxservices: 1.1
    cycler: 0.11.0
    Cython: 0.29.24
    decorator: 5.1.0
    docutils: 0.17.1
    et-xmlfile: 1.1.0
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 3.6.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.21
    imagecodecs: 2021.4.28
    imagesize: 1.3.0
    ipykernel: 5.5.5
    ipython: 7.23.1
    ipython-genutils: 0.2.0
    jedi: 0.18.0
    Jinja2: 3.0.1
    jupyter-client: 6.1.12
    jupyter-core: 4.9.1
    kiwisolver: 1.3.2
    lxml: 4.6.3
    lz4: 3.1.3
    MarkupSafe: 2.0.1
    matplotlib: 3.4.3
    matplotlib-inline: 0.1.3
    msgpack: 1.0.2
    netCDF4: 1.5.7
    networkx: 2.6.3
    numexpr: 2.8.0
    numpy: 1.21.2
    openpyxl: 3.0.9
    openvr: 1.16.801
    packaging: 21.3
    pandas: 1.4.2
    ParmEd: 3.2.0
    parso: 0.8.3
    pickleshare: 0.7.5
    Pillow: 8.3.2
    pip: 21.2.4
    pkginfo: 1.7.1
    prompt-toolkit: 3.0.23
    psutil: 5.8.0
    pycollada: 0.7.1
    pydicom: 2.1.2
    Pygments: 2.10.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.6
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.2
    pytz: 2021.3
    pywin32: 228
    pyzmq: 22.3.0
    qtconsole: 5.1.1
    QtPy: 1.11.3
    QtRangeSlider: 0.1.5
    RandomWords: 0.3.0
    requests: 2.26.0
    scipy: 1.7.1
    seaborn: 0.11.2
    setuptools: 57.5.0
    sfftk-rw: 0.7.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 4.2.0
    sphinx-autodoc-typehints: 1.12.0
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    suds-jurko: 0.6
    tables: 3.6.1
    tifffile: 2021.4.8
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.1.1
    urllib3: 1.26.7
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.0
    wheel-filename: 1.3.0
    WMI: 1.5.1

Change History (3)

comment:1 by pett, 3 years ago

Component: Unassigned → Third Party
Owner: set to Richard Scheltema
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → XMAS: KeyError: 'Score'

comment:2 by pett, 2 years ago

Resolution: → fixed
Status: assigned → closed

comment:3 by pett, 2 years ago

Fixed with newest release of XMAS (1.1.3)

Note: See TracTickets for help on using tickets.